Hyam tdwg LSID vocabulary http resolution

[Bob Morris]

Since these have never been ratified, what would be the objection to
deprecating the current resolution in favor of resolving and
dereferencing some svn-tagged version of the ontologies in
https://code.google.com/p/tdwg-ontology/ which on the 18th of December
will celebrate its 5th anniversary in its new home.

At the very least it would be useful to do this for those ontologies
modeling concerns of DwC, though it may be more robust to do them all
at once. It seems like not much to do, and even easy to version them
so if there is anyone using the old ones, they don't get burned.

In two projects we are investigating how much of those ontologies are
useful. In one for Plazi, Terry Catapano, with me looking on, is
building an ontology to unify legacy and prospective markup of
taxonomic treatments, and extraction of data from them. In another,
trying to open up the Euler taxonomy mapping application to play nice
with other applications, I am leaning on Nico Franz and other members
of the Euler team to see how much of Euler input and output we can
expresse in existing vocabularies. In an important case for Euler,
the google code is much more appropriate than the older one. This is
the case of relations between taxon concepts, wherein the old models
enumerations with instances right in the owl. Yech.

I'm willing to be an aggressive tester if we do this...

Bob



--
Robert A. Morris

Emeritus Professor of Computer Science
UMASS-Boston
100 Morrissey Blvd
Boston, MA 02125-3390


Filtered Push Project
Harvard University Herbaria
Harvard University

email: morri...@gmail.com
web: http://efg.cs.umb.edu/
web: http://wiki.filteredpush.org
http://wiki.datakurator.net
http://taxonconceptexplorer.org/
http://www.cs.umb.edu/~ram

[Steve Baskauf]

What does "deprecating the current resolution" mean? What resolution
are you talking about?

If we accepted the TDWG ontology, this is what we would get:
https://code.google.com/p/tdwg-rdf/wiki/BiodiversityOntologies#2_The_TDWG_Ontology
Most of the Darwin Core classes aren't there, so some people wouldn't
like that.

Also, it's loaded with domain and range declarations:
https://code.google.com/p/tdwg-rdf/wiki/BiodiversityOntologies#2.4_Some_object_properties
I thought you were against that.

There was also a consensus (I thought) at the TDWG 2013 meeting to note
that that the ontologies were no longer under development. Maybe also to
say that they were effectively deprecated, although I'd have to look for
meeting notes to verify that.

There is an additional question that is problematic. What does
tc:accordingTo mean? I have always assumed that it means what the
diagram in
https://code.google.com/p/tdwg-rdf/wiki/BiodiversityOntologies#2.2_Class_structure
shows. However, I had a recent email conversation with someone who
assumed (based on its text definition) that the object of tc:accordingTo
was a person or author team rather than a reference. I dug down into
the TCS XML schema (upon which the definition claims to be based) and
the answer still wasn't entirely clear. I can elaborate further if
anyone is interested. If it is a person and not a reference, then I
don't see how it can be used to represent taxon concepts the way most
people seem to be talking about them (a name plus a secundum reference).

There is a general problem that the only person who probably really
understands what the TDWG Ontologies really mean is Roger Hyam. He
never finished them (as can be seen by "todo" comments in several of the
ontologies) and no user documentation was ever written for them. And he
doesn't seem to be actively involved in TDWG any more.

Steve

Bob Morris wrote:
> Since these have never been ratified, what would be the objection to
> deprecating the current resolution in favor of resolving and
> dereferencing some svn-tagged version of the ontologies in
> https://code.google.com/p/tdwg-ontology/ which on the 18th of December
> will celebrate its 5th anniversary in its new home.
>
> At the very least it would be useful to do this for those ontologies
> modeling concerns of DwC, though it may be more robust to do them all
> at once. It seems like not much to do, and even easy to version them
> so if there is anyone using the old ones, they don't get burned.
>
> In two projects we are investigating how much of those ontologies are
> useful. In one for Plazi, Terry Catapano, with me looking on, is
> building an ontology to unify legacy and prospective markup of
> taxonomic treatments, and extraction of data from them. In another,
> trying to open up the Euler taxonomy mapping application to play nice
> with other applications, I am leaning on Nico Franz and other members
> of the Euler team to see how much of Euler input and output we can
> expresse in existing vocabularies. In an important case for Euler,
> the google code is much more appropriate than the older one. This is
> the case of relations between taxon concepts, wherein the old models
> enumerations with instances right in the owl. Yech.
>
> I'm willing to be an aggressive tester if we do this...
>
> Bob
>
>
>
>

--

Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

postal mail address:
PMB 351634
Nashville, TN 37235-1634, U.S.A.

delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235

office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 322-4942
If you fax, please phone or email so that I will know to look for it.
http://bioimages.vanderbilt.edu
http://vanderbilt.edu/trees

[Bob Morris]

Ah, my bad. I did something even worse than putting rdfs:domain on
predicates... :-) My very naughty thing was to propose a solution to
a problem I did not state. My problem, probably, is:

Problem: What http IRI should I assign to an ontology so that its
standard http resolution and dereference returns the rdf/xml available
when an svn checkout is applied to the svn object in the gcode svn
server at trunk/ontology/voc/TaxonConcept.owl

An answer seems to be:
http://tdwg-ontology.googlecode.com/svn/trunk/ontology/voc/TaxonConcept.owl
(*)

At the moment, I don't care if this is a good answer, any more than I
presently care whether or not the resolution and dereference of
http://rs.tdwg.org/ontology/voc/TaxonConcept provides something that
the community finds flawed. That is a separate conversation, in which
I did not mean to engage.

It would be helpful if someone put an svn tag on the current trunk in
the google code, in case, mirabile dictu, someone actually advances
the trunk beyond rev r18. (**)

--Bob
(*) This may seem a no-brainer, but AFAIK it works as a consequence
of the configuration of gcode's relation between its svn server and
its http server. It's common, but it doesn't happen automatically by
the gcode servers doing nothing except providing both http and svn
services.
(**) I think it's delicate and/or server-dependent to access prior svn
rev's with http, but perhaps I am wrong. Suggestion welcome.
Preferably with no '?' in the ontology IRI

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[John Wieczorek]

I have created a release in the tags directory at https://code.google.com/p/tdwg-ontology/source/browse/#svn%2Ftags%2Fv2009-12-18.